Isx low boost

I have a 99 isx 570, 600hp this truck sometimes will boost 35psi and run great. other times max boost will be 25psi run like crap and a knocking noise I assume is a air leak. I just put a new boost sensor in did not seem to make a difference. I do know the air charger has a small leak. Could that be doing that? I would think the boost would always be low not fluctuate. Sometimes when the truck idles it will lope other times it idles smooth. I just changed the ecm two months ago. The ecm and engine wanted a devorce they would not talk to each other. This engine was put in about 8mo. Ago my old one spun a Bearing. It has 400k on a pretty complete rebuild. My mechanic checked tjis engine out before install and told me it’s very tight that the knocking is not internal parts. Anyone have any ideas or is it probably the air charger?
Thanks

 

I was thinking along those lines guess I needed reassurance. When we put the engine in we changed three injectors. My mechanic said the others were not far behind.
Thanks